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wososa / PSI-Sigma

PSI-Sigma
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no .IR.out generated #26

Closed mhjiang97 closed 3 years ago

mhjiang97 commented 3 years ago

Hi,

I got an error when using PSI-Sigma.

ls afolder:

sample1.Aligned.sortedByCoord.out.bam
sample2.Aligned.sortedByCoord.out.bam
sample3.Aligned.sortedByCoord.out.bam
sample4.Aligned.sortedByCoord.out.bam
sample5.Aligned.sortedByCoord.out.bam
sample6.Aligned.sortedByCoord.out.bam
sample7.Aligned.sortedByCoord.out.bam
sample8.Aligned.sortedByCoord.out.bam
sample1.Aligned.sortedByCoord.out.bam.bai
sample2.Aligned.sortedByCoord.out.bam.bai
sample3.Aligned.sortedByCoord.out.bam.bai
sample4.Aligned.sortedByCoord.out.bam.bai
sample5.Aligned.sortedByCoord.out.bam.bai
sample6.Aligned.sortedByCoord.out.bam.bai
sample7.Aligned.sortedByCoord.out.bam.bai
sample8.Aligned.sortedByCoord.out.bam.bai
sample1.SJ.out.tab
sample2.SJ.out.tab
sample3.SJ.out.tab
sample4.SJ.out.tab
sample5.SJ.out.tab
sample6.SJ.out.tab
sample7.SJ.out.tab
sample8.SJ.out.tab
groupa.txt
groupb.txt
gencode.v32.annotation.primary_assembly.protein_coding2_sorted.gtf

cat afolder/groupa.txt:

sample1.Aligned.sortedByCoord.out.bam
sample2.Aligned.sortedByCoord.out.bam
sample3.Aligned.sortedByCoord.out.bam
sample4.Aligned.sortedByCoord.out.bam

cat afolder/groupb.txt:

sample5.Aligned.sortedByCoord.out.bam
sample6.Aligned.sortedByCoord.out.bam
sample7.Aligned.sortedByCoord.out.bam
sample8.Aligned.sortedByCoord.out.bam

the error:

gtf = gencode.v32.annotation.primary_assembly.protein_coding2_sorted.gtf
name = s1_s2
type = 1
nread = 5
skipratio = 0.05
fmode = 3
irmode = 0
adjp = 2
denominator = 1
irrange = 5
### NOTE: Staitistics::R and R are required.
Path = /usr/local/bin/PSI-Sigma-1.9k
sample1.Aligned.sortedByCoord.out.bam.bai is ready.
sample2.Aligned.sortedByCoord.out.bam.bai is ready.
sample3.Aligned.sortedByCoord.out.bam.bai is ready.
sample4.Aligned.sortedByCoord.out.bam.bai is ready.
sample5.Aligned.sortedByCoord.out.bam.bai is ready.
sample6.Aligned.sortedByCoord.out.bam.bai is ready.
sample7.Aligned.sortedByCoord.out.bam.bai is ready.
sample8.Aligned.sortedByCoord.out.bam.bai is ready.
Generating mapping file...
Checking splice-junction files...
===Splice-junction files spent 0.0000 hours.===
===Database spent 0.0000 hours.===
Getting intron reads....
Checking sample6.Aligned.sortedByCoord.out.bam...
Checking sample6.IR.out.tab...
Generating .IR.out for sample6
Processing sample6.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample8.Aligned.sortedByCoord.out.bam...
Checking sample8.IR.out.tab...
Generating .IR.out for sample8
Processing sample8.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample3.Aligned.sortedByCoord.out.bam...
Checking sample3.IR.out.tab...
Generating .IR.out for sample3
Processing sample3.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample1.Aligned.sortedByCoord.out.bam...
Checking sample1.IR.out.tab...
Generating .IR.out for sample1
Processing sample1.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample4.Aligned.sortedByCoord.out.bam...
Checking sample4.IR.out.tab...
Generating .IR.out for sample4
Processing sample4.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample2.Aligned.sortedByCoord.out.bam...
Checking sample2.IR.out.tab...
Generating .IR.out for sample2
Processing sample2.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample5.Aligned.sortedByCoord.out.bam...
Checking sample5.IR.out.tab...
Generating .IR.out for sample5
Processing sample5.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample7.Aligned.sortedByCoord.out.bam...
Checking sample7.IR.out.tab...
Generating .IR.out for sample7
Processing sample7.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
===Intron-read file spent 0.2756 hours.===
Ready to do PSI analysis...
===PSI analysis spent 0.0147 hours.===
Filtering ΔPSI results...
Aborting.. Can't open s1_s2_r5_ir3.txt : No such file or directory
Filtering mode = 3
Reading... gencode.v32.annotation.primary_assembly.protein_coding2_sorted.gtf.mapping.txt
Reading... s1_s2.db
===Filtering spent 0.0006 hours.===
Adjusting p-value distribution...
Aborting.. Can't open s1_s2_r5_ir3.sorted.txt : No such file or directory
Minimum number of samples for p-value = 2
Reading... s1_s2_r5_ir3.sorted.txt
===P-value adjustment spent 0.0008 hours.===

***Total: 0.2917 hours (or 17.502mins).

folder _wososatmp/ seems to be empty all the time when running PSI-Sigma with samtools 1.3.1, but with samtools 1.11 some tmp files were generated in _wososatmp/. However with samtools 1.11, the same error occurred.

required perl modules are installed and samtools version is 1.3.1.

Could you please help me to resolve it? Thanks a lot!

Best, Minghao

wososa commented 3 years ago

@mhjiang97 ,

Thanks for listing the detailed information. The gtf format gencode.v32.annotation.primary_assembly.protein_coding2_sorted.gtf might not be supported. I will suggest using Ensembl's gtf to do a test. Would you like to check this Docker version and identify missing pieces?

https://github.com/onuryukselen/PSI_Sigma_pipeline/tree/2.0

Please let me know if you still encounter issues.

Best, Woody